1. Which of the following is not the objective to perform sequence comparison?
a) To observe patterns of conservation
b) To find the common motifs present in both sequences
c) To study the physical properties of molecules
d) To study evolutionary relationships
Explanation: To assess whether it is likely that two sequences evolved from the same sequence comparison is required. Also, to find out which sequences from the database are similar to the sequence at hand, sequence comparison is carried out.
2. A dotplot is a visual and qualitative technique whereas the sequence alignment is an exact and quantitative measure of similarity of alignments.
a) True
b) False
Explanation: The sequence alignment is an exact and quantitative measure of similarity of alignments. It involves Construction of the best alignment between the sequences and assessment of the similarity from the alignment.
3. The global sequence alignment is suitable when the two sequences are of dissimilar length, with a negligible degree of similarity throughout.
a) true
b) false
Explanation: The global sequence alignment is suitable when the two sequences are of similar length, with a significant degree of similarity throughout. It gives the best alignment over the entire length of two sequences.
4. The alignment score is the sum of substitution scores and gap penalties in this type of algorithm.
a) true
b) false
Explanation: Use of +1 as a reward for a match, -1 as the penalty for a mismatch, and ignoring gaps is the scoring scheme of this type of method. Hence, the alignment score is the sum of substitution scores and gap penalties in this type of algorithm.
5. The substitution matrices are rarely used in this type of matching.
a) true
b) false
Explanation: The substitution matrices are quite commonly used in this type of matching. A concise way to express the residue substitution costs can be achieved with a N x N matrix where, N is 4 for DNA and 20 for proteins as 4 nucleotides in DNA and 20 amino acid residues in proteins are in picture respectively.
6. Which of the following is untrue about Protein substitution matrices?
a) They are significantly more complex than DNA scoring matrices
b) They have the N x N matrices of the amino acids
c) Protein substitution matrices have quite important role in evolutionary studies
d) They are significantly quite less complex than DNA scoring matrices
Explanation: Protein substitution matrices are significantly more complex than DNA scoring matrices. Proteins are composed of twenty amino acids, and physico-chemical properties of individual amino acids vary considerably. A protein substitution matrix can be based on any property of amino acids: size, polarity, charge, hydrophobicity.
7. In Needleman-Wunsch algorithm, the gaps are scored -2.
a) true
b) false
Explanation: In Needleman-Wunsch algorithm, the gaps are ignored. Amount of gap penalty is zero here. A gap corresponds to an insertion or a deletion of a Residue.
8. The number of possible global alignments between two sequences of length N is _____
a) \(\frac{2^N}{\sqrt{πN}}\)
b) \(\frac{2^{2N}}{\sqrt{πN}}\)
c) \(\frac{2^{(N-1)}}{\sqrt{πN}}\)
d) \(\frac{2^{2N}}{\sqrt{N}}\)
Explanation: By the total number of permutations and combinations option b gives the accurate number of possible global alignments between two sequences of length N. For two sequences of 250 residues this is 10149.
9. Which of the following is untrue about Needleman-Wunsch algorithm?
a) It is an example of dynamic programming
b) Basic idea here is to build up the best alignment by using optimal alignments of larger subsequences
c) It was first used by Saul Needleman and Christian Wunsch
d) It was first used in 1970
Explanation: In case of Needleman-Wunsch algorithm, the basic idea here is to build up the best alignment by using optimal alignments of smaller subsequences. It is based on dynamic programming, a discipline invented by Richard Bellman in 1953.
10. There are two types matrices involved in the study- score matrices and trace matrices
a) True
b) False
Explanation: The Needleman-Wunsch algorithm consists of three steps where these matrices play their role as follows:
i. Initialization of the score matrix
ii. Calculation of scores and filling the traceback matrix
iii. Deducing the alignment from the traceback matrix